Our modENCODE parent grant U01-HG004261 is aimed at annotating the functional short regulatory RNAs of Drosophila melanogaster using deep sequencing methodology. These include known classes of Argonaute-bound RNA such as microRNAs, small interfering RNAs, and piRNAs. In addition, potentially novel classes of RNAs may be uncovered as a result of this project. We request administrative supplemental funding to expand the range of our efforts to discover and annotate novel transcripts that represent or generate short regulatory RNAs in Drosophila. The bulk of the requested funds are dedicated to 50% salary support of a new bioinformatician to perform essential analyses of the large amount of small RNA data that we have produced for the consortium. We hope to uncover edited RNAs and species with untemplated additions, and to analyze non-canonical genic sources of mi/si/piRNAs. The remainder of the funds will be devoted towards novel methods for constructing and sequencing libraries that are enriched for normally labile primary microRNA transcripts. Their analysis should not only help to define microRNA gene structures, but may prove to reveal novel types of normally labile transcripts that might escape conventional RNA-seq efforts. U01-HG004261-03S1 Lai ARRA supplement